Assuming he's also got his Level 2 NVQ, he's more qualified than me. But quite how he made such a fundemental mistake...?
Unvented qualification is the G3 qualification,. No, he didn't go wrong because he's used to unvented cylinders - he's either a qualified idiot, or he's overtired and probably needs some time off, or he's unwell as Last Plumber suggests. Vented cylinders are one of the first things you learn about in plumbing courses as they are by far the most common type.
Trusting? Well, what else could you do? Ask too many questions and most plumbers will consider you untrusting and untrustworthy and won't want to work for you. You've been unlucky, that I admit.
From what I can see, while he's contaminated your cylinder feed cistern (which might or might not be the same as the cistern used to feed your upstairs cold tap, assuming your upstairs tap is not mains fed), all he'll have done as far as your boiler is concerned is connect it to the new and therefore relatively clean cylinder. Over time that might have led to the boiler scaling up, but it didn't work long enough for that to happen. I understand you'll want it checked out for reassurance, but a boiler service will probably not tell you very much (should really be serviced, or at least inspected, annually anyway).
If your boiler breaks tomorrow, you'll probably never know if it was cause or co-incidence. But my hunch is it won't break.
In any case, regardless of how well it was flushed five years ago, if the water is now black then there is dirt (usually corrosion products) in the system and this will tend to shorten the life of any boiler (although the old-fashioned boilers were built for robustness rather than efficiency and will tolerate dirtier water than modern ones).